Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer

The advance of experimental and computational techniques has allowed us to highlight the existence of numerous different mechanisms of RNA maturation, which have been so far unknown. Besides canonical splicing, consisting of the removal of introns from pre-mRNA molecules, non-canonical splicing events may occur to further increase the regulatory and coding potential of the human genome. Among these, splicing of microexons, recursive splicing and biogenesis of circular and chimeric RNAs through back-splicing and trans-splicing processes, respectively, all contribute to expanding the repertoire of RNA transcripts with newly acquired regulatory functions. Interestingly, these non-canonical splicing events seem to occur more frequently in the central nervous system, affecting neuronal development and differentiation programs with important implications on brain physiology. Coherently, dysregulation of non-canonical RNA processing events is associated with brain disorders, including brain tumours. Herein, we summarize the current knowledge on molecular and regulatory mechanisms underlying canonical and non-canonical splicing events with particular emphasis on cis-acting elements and trans-acting factors that all together orchestrate splicing catalysis reactions and decisions. Lastly, we review the impact of non-canonical splicing on brain physiology and pathology and how unconventional splicing mechanisms may be targeted or exploited for novel therapeutic strategies in cancer

Long-term culture of patient-derived cardiac organoids recapitulated Duchenne muscular dystrophy cardiomyopathy and disease progression

Duchenne Muscular Dystrophy (DMD) is an X-linked neuromuscular disease which to date is incurable. The major cause of death is dilated cardiomyopathy however, its pathogenesis is unclear as existing cellular and animal models do not fully recapitulate the human disease phenotypes. In this study, we generated cardiac organoids from patient-derived induced pluripotent stem cells (DMD-COs) and isogenic-corrected controls (DMD-Iso-COs) and studied if DMD-related cardiomyopathy and disease progression occur in the organoids upon long-term culture (up to 93 days). Histological analysis showed that DMD-COs lack initial proliferative capacity, displayed a progressive loss of sarcoglycan localization and high stress in endoplasmic reticulum. Additionally, cardiomyocyte deterioration, fibrosis and aberrant adipogenesis were observed in DMD-COs over time. RNA sequencing analysis confirmed a distinct transcriptomic profile in DMD-COs which was associated with functional enrichment in hypertrophy/dilated cardiomyopathy, arrhythmia, adipogenesis and fibrosis pathways. Moreover, five miRNAs were identified to be crucial in this dysregulated gene network. In conclusion, we generated patient-derived cardiac organoid model that displayed DMD-related cardiomyopathy and disease progression phenotypes in long-term culture. We envision the feasibility to develop a more complex, realistic and reliable in vitro 3D human cardiac-mimics to study DMD-related cardiomyopathies

Gene expression profile of rat left ventricles reveals persisting changes following chronic mild exercise protocol: implications for cardioprotection

<p>Abstract</p> <p>Background</p> <p>Epidemiological studies showed that physical exercise, specifically moderate lifelong training, is protective against cardiovascular morbidity and mortality. Most experimental work has focused into the effects and molecular mechanisms underlying intense, rather than mild exercise, by exploring the acute effect of training. Our study aims at investigating the cardioprotective effect of mild chronic exercise training and the gene expression profile changes at 48 hrs after the exercise cessation. Rats were trained at mild intensity on a treadmill: 25 m/min, 10%incline, 1 h/day, 3 days/week, 10 weeks; about 60% of the maximum aerobic power. By Affymetrix technology, we investigated the gene expression profile induced by exercise training in the left ventricle (LV) of trained (n = 10) and control (n = 10) rats. Cardioprotection was investigated by ischemia/reperfusion experiments (n = 10 trained vs. n = 10 control rats).</p> <p>Results</p> <p>Mild exercise did not induce cardiac hypertrophy and was cardioprotective as demonstrated by the decreased infarct size (p = 0.02) after ischemia/reperfusion experiments in trained with respect to control rats. Ten genes and 2 gene sets (two pathways) resulted altered in LV of exercised animals with respect to controls. We validated by real-time PCR the increased expression of four genes: similar to C11orf17 protein (RGD1306959), caveolin 3, enolase 3, and hypoxia inducible factor 1 alpha. Moreover, caveolin 3 protein levels were higher in exercised than control rats by immunohistochemistry and Western Blot analysis. Interestingly, the predicted gene similar to C11orf17 protein (RGD1306959) was significantly increased by exercise. This gene has a high homology with the human C11orf17 (alias: protein kinase-A interacting protein 1 or breast cancer associated gene 3). This is the first evidence that this gene is involved in the response to the exercise training.</p> <p>Conclusion</p> <p>Our data indicated that few, but significant, genes characterize the gene expression profile of the rat LV, when examined 48 hrs since the last training section and that mild exercise training determines cardioprotection without the induction of hypertrophy.</p

Effects of Prunus cerasus L. Seeds and Juice on Liver Steatosis in an Animal Model of Diet-Induced Obesity

The accumulation of adipose tissue increases the risk of several diseases. The fruits-intake, containing phytochemicals, is inversely correlated with their development. This study evaluated the effects of anthocyanin-rich tart cherries in diet-induced obese (DIO) rats. DIO rats were exposed to a high-fat diet with the supplementation of tart cherry seeds powder (DS) and seed powder plus juice (DJS). After 17 weeks, the DIO rats showed an increase of body weight, glycaemia, insulin, and systolic blood pressure. In the DS and DJS groups, there was a decrease of systolic blood pressure, glycaemia, triglycerides, and thiobarbituric reactive substances in the serum. In the DJS rats, computed tomography revealed a decrease in the spleen-to-liver attenuation ratio. Indeed, sections of the DIO rats presented hepatic injury characterized by steatosis, which was lower in the supplemented groups. In the liver of the DIO compared with rats fed with a standard diet (CHOW), a down-regulation of the GRP94 protein expression and a reduction of LC3- II/LC3-I ratio were found, indicating endoplasmic reticulum stress and impaired autophagy flux. Interestingly, tart cherry supplementation enhanced both unfolded protein response (UPR) and autophagy. This study suggests that tart cherry supplementation, although it did not reduce body weight in the DIO rats, prevented its related risk factors and liver steatosis

Effects of Prunus cerasus L. Seeds and Juice on Liver Steatosis in an Animal Model of Diet-Induced Obesity

The accumulation of adipose tissue increases the risk of several diseases. The fruits-intake, containing phytochemicals, is inversely correlated with their development. This study evaluated the effects of anthocyanin-rich tart cherries in diet-induced obese (DIO) rats. DIO rats were exposed to a high-fat diet with the supplementation of tart cherry seeds powder (DS) and seed powder plus juice (DJS). After 17 weeks, the DIO rats showed an increase of body weight, glycaemia, insulin, and systolic blood pressure. In the DS and DJS groups, there was a decrease of systolic blood pressure, glycaemia, triglycerides, and thiobarbituric reactive substances in the serum. In the DJS rats, computed tomography revealed a decrease in the spleen-to-liver attenuation ratio. Indeed, sections of the DIO rats presented hepatic injury characterized by steatosis, which was lower in the supplemented groups. In the liver of the DIO compared with rats fed with a standard diet (CHOW), a down-regulation of the GRP94 protein expression and a reduction of LC3- II/LC3-I ratio were found, indicating endoplasmic reticulum stress and impaired autophagy flux. Interestingly, tart cherry supplementation enhanced both unfolded protein response (UPR) and autophagy. This study suggests that tart cherry supplementation, although it did not reduce body weight in the DIO rats, prevented its related risk factors and liver steatosis

Framing Cutting-Edge Integrative Deep-Sea Biodiversity Monitoring via Environmental DNA and Optoacoustic Augmented Infrastructures

17 pages, 1 figure, 1 tableDeep-sea ecosystems are reservoirs of biodiversity that are largely unexplored, but their exploration and biodiscovery are becoming a reality thanks to biotechnological advances (e.g., omics technologies) and their integration in an expanding network of marine infrastructures for the exploration of the seas, such as cabled observatories. While still in its infancy, the application of environmental DNA (eDNA) metabarcoding approaches is revolutionizing marine biodiversity monitoring capability. Indeed, the analysis of eDNA in conjunction with the collection of multidisciplinary optoacoustic and environmental data, can provide a more comprehensive monitoring of deep-sea biodiversity. Here, we describe the potential for acquiring eDNA as a core component for the expanding ecological monitoring capabilities through cabled observatories and their docked Internet Operated Vehicles (IOVs), such as crawlers. Furthermore, we provide a critical overview of four areas of development: (i) Integrating eDNA with optoacoustic imaging; (ii) Development of eDNA repositories and cross-linking with other biodiversity databases; (iii) Artificial Intelligence for eDNA analyses and integration with imaging data; and (iv) Benefits of eDNA augmented observatories for the conservation and sustainable management of deep-sea biodiversity. Finally, we discuss the technical limitations and recommendations for future eDNA monitoring of the deep-sea. It is hoped that this review will frame the future direction of an exciting journey of biodiscovery in remote and yet vulnerable areas of our planet, with the overall aim to understand deep-sea biodiversity and hence manage and protect vital marine resourcesThis research has been funded within the framework of the following project activities: ARIM (Autonomous Robotic Sea-Floor Infrastructure for Benthopelagic Monitoring; MarTERA ERA-Net Cofound); RESBIO (TEC2017-87861-R; Ministerio de Ciencia, Innovación y Universidades); JERICO-S3: (Horizon 2020; Grant Agreement no. 871153); ENDURUNS (Research Grant Agreement H2020-MG-2018-2019-2020 n.824348); Slovenian Research Agency (Research Core Funding Nos. P1-0237 and P1-0255 and project ARRS-RPROJ-JR-J1-3015). We also profited of the funding from the Spanish Government through the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S) and Italian Ministry of Education (MIUR) under the “Bando premiale FOE 2015” (nota prot. N. 850, dd. 27 ottobre 2017) with the project EarthCruisers “EARTH’s CRUst Imagery for Investigating Seismicity, Volcanism, and Marine Natural Resources in the Sicilian Offshore”. Ocean Networks Canada was funded through Canada Foundation for Innovation-Major Science Initiative (CFI-MSI) fund 30199Peer reviewe

Framing Cutting-Edge Integrative Deep-Sea Biodiversity Monitoring via Environmental DNA and Optoacoustic Augmented Infrastructures

Deep-sea ecosystems are reservoirs of biodiversity that are largely unexplored, but their exploration and biodiscovery are becoming a reality thanks to biotechnological advances (e.g., omics technologies) and their integration in an expanding network of marine infrastructures for the exploration of the seas, such as cabled observatories. While still in its infancy, the application of environmental DNA (eDNA) metabarcoding approaches is revolutionizing marine biodiversity monitoring capability. Indeed, the analysis of eDNA in conjunction with the collection of multidisciplinary optoacoustic and environmental data, can provide a more comprehensive monitoring of deep-sea biodiversity. Here, we describe the potential for acquiring eDNA as a core component for the expanding ecological monitoring capabilities through cabled observatories and their docked Internet Operated Vehicles (IOVs), such as crawlers. Furthermore, we provide a critical overview of four areas of development: (i) Integrating eDNA with optoacoustic imaging ; (ii) Development of eDNA repositories and cross-linking with other biodiversity databases ; (iii) Artificial Intelligence for eDNA analyses and integration with imaging data ; and (iv) Benefits of eDNA augmented observatories for the conservation and sustainable management of deep-sea biodiversity. Finally, we discuss the technical limitations and recommendations for future eDNA monitoring of the deep-sea. It is hoped that this review will frame the future direction of an exciting journey of biodiscovery in remote and yet vulnerable areas of our planet, with the overall aim to understand deep-sea biodiversity and hence manage and protect vital marine resources

Obesity-related nervous system injury: preliminary evidences in diet induced obesity (DIO) rats.

Increased food intake, reduced physical activity and altered metabolic processes are the variables that affect energy balance inducing obesity. Obesity is now considered an increas-ingly medical challenge. Actually, the prevalence of obesity has increased dramatically worldwide over the last decades and has now reached epidemic proportions. On the other hand, obesity is associated with the development of chronic diseases such as cerebrovascu-lar disease promoting the cognitive decline. Caloric-dense diet induced obesity (DIO), provides a useful animal model sharing several common features with human obesity. DIO rats of 7 weeks of age are expose to high fat (45 %) diet ad libitum and after 5 weeks the obese phenotype starts to be develop. To clarify the possible relationships between obesity and nervous system changes, DIO rats were studied after 5 weeks and 17 weeks of hypercaloric diet compared to the control rats with not fat diet (Chow). Memory performance were measured using different cognitive tests. Moreover, ultrasonographic (US) and computed tomography (CT) evaluations were per-formed to detect adipose tissue changes. Magnetic resonance imaging (MRI) to highlight brain morphological alterations was used. Morphological changes of brain areas (frontal cor-tex, hippocampus) were evaluated by immunohistochemical analysis. The results confirmed the developed of obesity after 5 weeks of fat diet. At long-term (17 weeks) high fat diet exposure, rats increased significantly their body weight in comparison to the control group and the youngest DIO rats. The US and CT analysis indicated an increase of deposition of both visceral and subcutaneous adipose tissue and evidences a decrease of hepatic attenuation in the older DIO rats.MRI images did not show vascular and morphologi-cal alterations in brain. Instead, immuhistochemical and immunochemical analysis, revealed an increase expression of glial-fibrillary acidic protein (GFAP) in the older DIO rats compared to the age- matched Chow rats both in frontal cortex and in hippocampus. DIO rats showed a reduction of retention latency time in the emotional learning task. These preliminary findings indicate that the development of obesity, does not determined gross anatomy alteration in brain, but the occurrence of injury characterized by astrogliosis. The identification of neurodegenerative changes in DIO may represent the first insight to better characterize the neuronal involvement in obesity

Obesity affects central nervous system: a multidisciplinary study in Diet-Induced Obesity (DIO) rats

Obesity has doubled worldwide in the last thirty years, becoming pandemic [1]. Overconsumption of energy-dense food is advanced as the major explanation for the current increase of overweight and obesity, including for children and adolescents [2]. Obesity represents also an independent risk factor for the development of cerebrovascular disease and cognitive impairment. The systemic effects, such as increased fat mass, hypertension, insulin resistance and general metabolic dysfunction, have been identified as factors that may lead to im-paired cognitive function [3]. In humans, obesity is associated with cognitive deficits, especially de-clarative memory which depends on the hippocampus [4]. To clarify the possible relationships between obesity and nervous system changes, high-caloric Diet-Induced Obesity (DIO) rats were studied after 5 weeks and 17 weeks of hypercaloric diet com-pared to the control rats with not fat diet (Chow) or to rats not developing obesity (DIO-resistant DR). DIO rats of 7 weeks of age were exposed to specific diet ad libitum and after 5 weeks the ob-ese phenotype starts to develop. Food consumption, fat mass content, blood pressure, fasting insulin and glucose levels were moni-tored. The behavioral analysis included locomotor activity and anxiety-like behavior test, novel ob-ject recognition test, spatial learning, and memory test were performed. Magnetic resonance imaging (MRI) in the brain was performed to investigate possible gross anatomical changes. RT-PCR, immunochemical and immunohistochemical analysis were performed to evaluate neuronal and glial alterations. After long-term high fat diet exposure, body weight was remarkably increased in DIO rats com-pared to the control group and DR rats. Glycaemia was higher in DIO rats only after 17 weeks of the high fat diet. No differences in values of total cholesterol and triglycerides were observed. Sys-tolic blood pressure was higher in DIO rats only after 17 weeks of high-fat diet compared to age-matched Chow rats and DR rats. Furthermore increased oxidative stress was observed in the serum of DIO rats compared to Chow rats. The open-field test revealed, in the older DIO rats, a decrease of cumulative distance traveled, their number of rearings and increasing the total immobility time. Only older DIO rats showed a reduc-tion of retention latency time in the passive avoidance test. MRI did not show significant morpho-logical and vascular brain changes. Immunohistochemical and immunochemical analysis showed an increased expression of the glial-fibrillary acid protein in the frontal cortex and hippocampus of older DIO rats compared to age-matched Chow and DR rats. A decrease of neurofilament expression was found in the hippocampus of older DIO rats without decrease of the number of neurons. RT-qPCR analysis revealed a modula-tion in the Transient Receptor Potential (TRP) channels and synaptic components. These results indicate that obesity in rats, in addition to the development of correlate cerebrovascu-lar risk factors, causes brain injury characterized by astrogliosis, neurodegeneration and impaired learning and memory tasks. The identification of neurodegenerative changes in DIO rats may represent the first step to better characterize the neuronal modifications occurring in the obesity and propose pharmacological treatments or food strategies to counteract them. [1] WHO, World health Organisation, 2013. http://www.who.int/mediacentre/factsheets/fs311/en/ [2] R.B. Ervin, C.L. Ogden. Trends in intake of energy and macronutrients in children and adoles-cents from 1999–2000 through 2009–2010. NCHS Data Brief 2013, 113, 1 [3] R.M. Uranga, A.J. Bruce-Keller, C.D. Morrison, S.O. Fernandez-Kim, P.J. Ebenezer, et al.. In-tersection between metabolic dysfunction, high fat diet consumption, and brain aging. J Neurochem 2010, 114, 344 [4] H. Francis, R. Stevenson. The longer-term impacts of Western diet on human cognition and the brain. Appetite 2013, 63, 11